Background: Physical fitness is one of the most important qualities in armed forces personnel. However, little is known about the association between the military environment and the occupational and leisure-time dimensions of the physical activity practiced there. This study assessed the association of rank, job stress and psychological distress with physical activity levels (overall and by dimensions). Methods: This a cross-sectional study among 506 military service personnel of the Brazilian Army examined the association of rank, job stress and psychological distress with physical activity through multiple linear regression using a generalized linear model. Results: The adjusted models showed that the rank of lieutenant was associated with most occupational physical activity (β = 0.324; CI 95% 0.167; 0.481); “high effort and low reward” was associated with more occupational physical activity (β = 0.224; CI 95% 0.098; 0.351) and with less physical activity in sports/physical exercise in leisure (β = −0.198; CI 95% −0.384; −0.011); and psychological distress was associated with less physical activity in sports/exercise in leisure (β = −0.184; CI 95% −0.321; −0.046). Conclusions: The results of this study show that job stress and rank were associated with higher levels of occupational physical activity. Moreover job stress and psychological distress were associated with lower levels of physical activity in sports/exercises. In the military context, given the importance of physical activity and the psychosocial environment, both of which are related to health, these findings may offer input to institutional policies directed to identifying psychological distress early and improving work relationships, and to creating an environment more favorable to increasing the practice of leisure-time physical activity.